Microarrays with toxicologically relevant genes (tox genes) have been developed in our laboratory for toxicogenomics studies in rat, dog and man. The genes were chosen using published information as well as a discovery process for genes responsive to toxic treatments using transcription profiling experiments conducted with rats and dogs. In addition to published information human tox genes were derived from rat tox genes based on gene homology. Using the microarray with rat-specific tox genes, a database containing gene expression, histopathology, and clinical chemistry findings has been generated for 89 compounds. Analysis of the database indicates that treatment with toxic compounds induces specific gene expression patterns. Dose- and time-dependent response relationships in gene expression were observed for treatment with toxic compounds. Gene expression at 24h was found to correlate well with organ toxicity observed at 72 h. Mining of the database led to the selection of specific groups of genes (predictive gene sets) whose expression patterns are predictive of organ toxicity with a high degree of accuracy (approximately 90%). The data also provide insight on toxic mechanism and gene regulation pathways. For instance, carbon tetrachloride and chloroform treatments were found to decrease the expression of the cytochrome P450 isoform 3A1 gene while enhancing the expression of the multiple drug resistance gene MDR1 in liver, clearly demonstrating that the CYP3A1 and MDR1 genes were not co-regulated as postulated by some researchers. This approach, the use of gene expression as an endpoint to define organ toxicity, is extended to the definition of human drug toxicity using primary human hepatocytes as a test system. Preliminary results demonstrate that the toxic drug, troglitazone, can be clearly distinguished from the less toxic analogues, rosiglitazone and pioglitazone based on their effects on tox gene expression in human hepatocytes. Our results with both rats in vivo and human hepatocytes in vitro suggest that microarrays with toxicologically relevant genes can be used routinely for the evaluation of chemical toxicity.